Hi There
I still have problem with recording VAT payments in QB. As a result, the Total Current Liabilities in my company's balance sheet is much higher that it should be. I wonder if anybody have a solution for this problem?
I'll make sure you can record your historic VAT payments in QuickBooks Online (QBO), @mkhalilpour. This way, your total current liabilities in your company's balance sheet will show an accurate amount and keep your financial data updated.
When you've filed VAT returns outside QuickBooks, you can create an expense transaction to record your payments to HMRC. To do this, you'll first have to create an expense account to track your VAT payments. Make sure to select the appropriate information in the Account (i.e., Expenses) and Detail Type (i.e., Taxes Paid) fields. Please see the screenshot below for your reference.

Once you're done, record an Expense transaction from the + New button. You'll have to make sure to select the VAT agency name from the Payee drop-down, then choose the expense account (i.e., Taxes Paid) and all other payment details in the Category details section.

Since you've already imported the last 2 years' worth of transactions to your current bank account (including the VAT payments), you'll need to match the expenses you've created in QBO. This way, you can keep your books accurate. For the step-by-step guide, you can refer to this article: Categorise online bank transactions in QuickBooks Online.
To know more about filing VAT returns and recording payments in QBO, I'd recommend checking out this article: File your VAT return and record tax payment in QuickBooks Online.
Then, pull up the Balance Sheet report to make sure the data you've entered are recorded accordingly. To do this, go to the Business overview section from the Reports menu's Standard tab.
Also, to further guide you in managing your VAT payments and submitting returns to HMRC, I'd recommend checking out these articles:
Keep me posted on how it goes in the comments below. If you have other concerns about managing VAT payments in QBO, I'll gladly help. Take care, and I wish you continued success, @mkhalilpour.